Inside Your Gut: Understanding Your Gut Microbiome

Written By Savannah Cass

You’ve probably heard the term gut microbiome everywhere lately, on social media, in wellness podcasts, maybe even from your doctor. But what does it actually mean? And why does it matter so much, especially if you’re dealing with IBS?

Let’s break it down in a way that actually makes sense.

So… what is the gut microbiome?

Your gut microbiome is a massive community of microorganisms, mostly bacteria, but also fungi, viruses, and other microbes, living throughout your digestive tract. The majority of them reside in your colon.

We’re talking trillions of microbes forming a complex internal ecosystem. There are actually more bacteria in your body than there are human cells. 

Think of it like a bustling city inside your gut:

  • Some microbes are helpful

  • Some are neutral

  • Some can cause problems if they get out of balance

Each person’s microbiome is unique, like a fingerprint.

And… interestingly enough you inherit part of your microbiome from your family. Meaning certain bacterial strains can run in families. Crazy, right?!  But your lifestyle and diet plays a huge role in shaping it over time and alters your “core” gut microbiota. 

Things that influence your microbiome include:

  • Diet

  • Whether you were breastfed

  • Antibiotic use

  • Environment and lifestyle habits

For example, repeated antibiotic use can wipe out certain beneficial bacteria, sometimes permanently.

A healthy microbiome isn’t about having “perfect” bacteria. It’s about diversity and balance, a wide variety of microbes living in a stable ecosystem.

So, what does your microbiome actually do?

The short answer: A LOT 

1. Breaks down food you can’t digest on your own
Certain fibers and resistant starches can’t be digested by your body alone. Your gut bacteria step in to ferment these foods, producing beneficial compounds like short-chain fatty acids that support your intestinal lining and are anti-inflammatory. 

2. Supports your immune system
Around 70% of your immune system lives in your gut. Your microbiome helps train your immune system to know what’s harmful and what’s not, reducing unnecessary inflammation. It also helps protect against allergy development. 

3. Produces important nutrients
Some gut bacteria produce vitamins like B vitamins and vitamin K, which are essential for energy and overall health. The gut microbes also help assist in mineral absorption, like calcium, magnesium, and zinc. 

4. Communicates with your brain
The gut and brain are closely connected through what’s called the gut-brain axis. Your microbiome plays a role in mood, your response to stress, and even mental clarity.

5. Regulates gut motility

Your microbiome helps control how quickly food moves through your digestive tract.

Slow motility → constipation                    Fast motility → diarrhea

What happens when things get out of balance?

An imbalanced microbiome is called dysbiosis. Dysbiosis is defined as changes in the intestinal flora and their metabolic activities that produce harmful effects on the host (that’s you!). And dysbiosis is believed to play a role in SO many chronic diseases, including:

Digestive conditions:

  • IBS

  • Celiac disease

  • Inflammatory bowel disease (IBD)

  • SIBO

  • Diverticulitis

  • Fatty liver disease

Beyond the gut:

  • Anxiety and depression

  • Chronic fatigue

  • Asthma

  • Obesity

  • Neurodegenerative diseases like Alzheimer’s and Parkinson’s

What affects your microbiome?

Your microbiome is constantly evolving, but big changes require consistent habits over time.

Key factors include:

  • What you eat (especially fiber and plant diversity)

  • Stress levels

  • Sleep quality

  • Antibiotic use

  • Physical activity

One important note:

A diet high in fat and protein (like “dirty keto” and carnivore diet) but low in fiber and plant foods can significantly shift your microbiome. Over time, beneficial fiber and plant-loving microbes can decline, or even disappear. 

This can:

  • Reduce your ability to tolerate a variety of foods

  • Make it harder to restore a healthy microbiome later

Why the microbiome matters for IBS

If you have IBS (Irritable Bowel Syndrome), your microbiome may be out of balance.

This can contribute to:

  • Visceral hypersensitivity (increased gut sensitivity, leading to pain)

  • Irregular motility (constipation, diarrhea, or both)

  • Stress-related gut dysfunction

Bottom line

A healthy microbiome is essential for overall health, especially gut health.

  • A healthy and balanced microbiota is absolutely essential for overall health, and especially gut health 

  • Your microbiome influences every system in your body

  • What you eat directly feeds your microbes, and shapes your health

If you’d like personalized support, feel free to book an appointment with me to test your gut microbiome and work on optimizing it together. 

Savannah Cass
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